Workflow: 03-map-se.cwl

Fetched 2019-03-19 00:35:44 GMT

ChIP-seq 03 mapping - reads: SE

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Inputs

ID Type Title Doc
genome_sizes_file File

Genome sizes tab-delimited file (used in samtools)

picard_jar_path String

Picard Java jar file

genome_ref_first_index_file File

Bowtie first index files for reference genome (e.g. *1.ebwt). The rest of the files should be in the same folder.

ENCODE_blacklist_bedfile File

Bedfile containing ENCODE consensus blacklist regions to be excluded.

nthreads Integer
input_fastq_files File[]

Input fastq files

picard_java_opts String (Optional)

JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")

Steps

ID Runs Label Doc
preseq-c-curve
../map/preseq-c_curve.cwl (CommandLineTool)

Usage: c_curve [OPTIONS] <sorted-bed-file>

Options: -o, -output yield output file (default: stdout) -s, -step step size in extrapolations (default: 1e+06) -v, -verbose print more information -P, -pe input is paired end read file -H, -hist input is a text file containing the observed histogram -V, -vals input is a text file containing only the observed counts -B, -bam input is in BAM format -l, -seg_len maximum segment length when merging paired end bam reads (default: 5000)

Help options: -?, -help print this help message -about print about message

masked_file_basename
../utils/extract-basename.cwl (CommandLineTool)

Extracts the base name of a file

filter-unmapped
../map/samtools-filter-unmapped.cwl (CommandLineTool)
sort_bams
../map/samtools-sort.cwl (CommandLineTool)
sort_dups_marked_bams
../map/samtools-sort.cwl (CommandLineTool)
remove_duplicates
../map/samtools-view.cwl (CommandLineTool)
index_dedup_bams
../map/samtools-index.cwl (CommandLineTool)
mapped_reads_count
../map/bowtie-log-read-count.cwl (CommandLineTool)

Get number of processed reads from Bowtie log.

remove_encode_blacklist
../map/bedtools-intersect.cwl (CommandLineTool)

Tool: bedtools intersect (aka intersectBed) Version: v2.25.0 Summary: Report overlaps between two feature files.

Usage: bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>

Note: -b may be followed with multiple databases and/or wildcard (*) character(s). Options: -wa Write the original entry in A for each overlap.

-wb Write the original entry in B for each overlap. - Useful for knowing _what_ A overlaps. Restricted by -f and -r.

-loj Perform a \"left outer join\". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B.

-wo Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlaps restricted by -f and -r. Only A features with overlap are reported.

-wao Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlapping features restricted by -f and -r. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.

-u Write the original A entry _once_ if _any_ overlaps found in B. - In other words, just report the fact >=1 hit was found. - Overlaps restricted by -f and -r.

-c For each entry in A, report the number of overlaps with B. - Reports 0 for A entries that have no overlap with B. - Overlaps restricted by -f and -r.

-v Only report those entries in A that have _no overlaps_ with B. - Similar to \"grep -v\" (an homage).

-ubam Write uncompressed BAM output. Default writes compressed BAM.

-s Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand.

-S Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand.

-f Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)

-F Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)

-r Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90 percent of A and A _also_ overlaps 90 percent of B.

-e Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90 percent of A is covered OR 10 percent of B is covered. Without -e, both fractions would have to be satisfied.

-split Treat \"split\" BAM or BED12 entries as distinct BED intervals.

-g Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option.

-nonamecheck For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. \"chr1\" vs \"chr01\".

-sorted Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.

-names When using multiple databases, provide an alias for each that will appear instead of a fileId when also printing the DB record.

-filenames When using multiple databases, show each complete filename instead of a fileId when also printing the DB record.

-sortout When using multiple databases, sort the output DB hits for each record.

-bed If using BAM input, write output as BED.

-header Print the header from the A file prior to results.

-nobuf Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time.

-iobuf Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files.

Notes: (1) When a BAM file is used for the A file, the alignment is retained if overlaps exist, and exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not reported, as we are only testing for one or more overlaps.

filtered2sorted
../map/samtools-sort.cwl (CommandLineTool)
mark_duplicates
../map/picard-MarkDuplicates.cwl (CommandLineTool)
percent_uniq_reads
../map/preseq-percent-uniq-reads.cwl (CommandLineTool)

Get number of processed reads from Bowtie log.

sort_dedup_bams
../map/samtools-sort.cwl (CommandLineTool)
execute_pcr_bottleneck_coef

ChIP-seq - map - PCR Bottleneck Coefficients

sam2bam
../map/samtools2bam.cwl (CommandLineTool)
mapped_filtered_reads_count
../peak_calling/samtools-extract-number-mapped-reads.cwl (CommandLineTool)

Extract mapped reads from BAM file using Samtools flagstat command

sort_masked_bams
../map/samtools-sort.cwl (CommandLineTool)
index_masked_bams
../map/samtools-index.cwl (CommandLineTool)
index_dups_marked_bams
../map/samtools-index.cwl (CommandLineTool)
extract_basename_2
../utils/remove-extension.cwl (CommandLineTool)

Extracts the base name of a file

extract_basename_1
../utils/extract-basename.cwl (CommandLineTool)

Extracts the base name of a file

bowtie-se
../map/bowtie-se.cwl (CommandLineTool)

Outputs

ID Type Label Doc
output_picard_mark_duplicates_files File[]

Picard MarkDuplicates metrics files.

output_read_count_mapped_filtered File[]

Read counts of the mapped and filtered BAM files

output_data_sorted_dedup_bam_files File[]

BAM files without duplicate reads, sorted and indexed.

output_percentage_uniq_reads File[]

Percentage of uniq reads from preseq c_curve output

output_read_count_mapped File[]

Read counts of the mapped BAM files

output_preseq_c_curve_files File[]

Preseq c_curve output files.

output_pbc_files File[]

PCR Bottleneck Coeficient files.

output_data_sorted_dups_marked_bam_files File[]

BAM files with duplicate reads flagged using picard MarkDuplicates, sorted and indexed.

output_bowtie_log File[]

Bowtie log file.

Permalink: https://w3id.org/cwl/view/git/6d9457382f0b7cc2510e148d21383261280d17ed/v1.0/ChIP-seq_pipeline/03-map-se.cwl